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  <div class="section" id="tutorials">
<h1>Tutorials<a class="headerlink" href="#tutorials" title="Permalink to this headline">¶</a></h1>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="0._Unit_conversions.html">0. Unit conversions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="0._Unit_conversions.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="0._Unit_conversions.html#2.-Basics">2. Basics</a></li>
<li class="toctree-l2"><a class="reference internal" href="0._Unit_conversions.html#3.-Data-model-representations">3. Data model representations</a></li>
<li class="toctree-l2"><a class="reference internal" href="0._Unit_conversions.html#4.-Unit-debugging">4. Unit debugging</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="1._Defining_atomic_systems.html">1. Defining atomic systems</a><ul>
<li class="toctree-l2"><a class="reference internal" href="1._Defining_atomic_systems.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="1._Defining_atomic_systems.html#2.-Create-a-System">2. Create a System</a></li>
<li class="toctree-l2"><a class="reference internal" href="1._Defining_atomic_systems.html#3.-Load-a-System">3. Load a System</a></li>
<li class="toctree-l2"><a class="reference internal" href="1._Defining_atomic_systems.html#4.-System-Manipulations">4. System Manipulations</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="1.1._Box_class.html">1.1. Box class</a><ul>
<li class="toctree-l2"><a class="reference internal" href="1.1._Box_class.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.1._Box_class.html#2.-Box-parameters">2. Box parameters</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.1._Box_class.html#3.-Initializing-and-setting-Box-parameters">3. Initializing and setting Box parameters</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.1._Box_class.html#4.-LAMMPS-compatible-Boxes">4. LAMMPS-compatible Boxes</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.1._Box_class.html#5.-Box-model">5. Box model</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.1._Box_class.html#6.-Inside/outside">6. Inside/outside</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="1.2._Atoms_class.html">1.2. Atoms class</a><ul>
<li class="toctree-l2"><a class="reference internal" href="1.2._Atoms_class.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.2._Atoms_class.html#2.-Basics">2. Basics</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.2._Atoms_class.html#3.-Per-atom-properties">3. Per-atom properties</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.2._Atoms_class.html#4.-Atoms-by-index">4. Atoms by index</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.2._Atoms_class.html#5.-Atoms.extend()">5. Atoms.extend()</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.2._Atoms_class.html#6.-Atoms.prop()">6. Atoms.prop()</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.2._Atoms_class.html#7.-Atoms.prop_atype()">7. Atoms.prop_atype()</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.2._Atoms_class.html#8.-Atoms.model()">8. Atoms.model()</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="1.3._System_class.html">1.3. System class</a><ul>
<li class="toctree-l2"><a class="reference internal" href="1.3._System_class.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.3._System_class.html#2.-Basics">2. Basics</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.3._System_class.html#3.-Built-in-Attributes">3. Built-in Attributes</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.3._System_class.html#4.-Scaling-Additions">4. Scaling Additions</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.3._System_class.html#5.-Built-in-manipulations">5. Built-in manipulations</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.3._System_class.html#6.-Built-in-analysis-tools">6. Built-in analysis tools</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.3._System_class.html#7.-model()-and-dump()">7. model() and dump()</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="1.4._Load_and_dump_conversions.html">1.4. Load and dump conversions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="1.4._Load_and_dump_conversions.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.4._Load_and_dump_conversions.html#2.-Load">2. Load</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.4._Load_and_dump_conversions.html#3.-Dump">3. Dump</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.4._Load_and_dump_conversions.html#4.-Supported-styles">4. Supported styles</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="1.4.1._system_model_conversions.html">1.4.1. system_model conversions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="1.4.1._system_model_conversions.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.4.1._system_model_conversions.html#2.-Dump">2. Dump</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.4.1._system_model_conversions.html#3.-Load">3. Load</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="1.4.2._POSCAR_conversions.html">1.4.2. POSCAR conversions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="1.4.2._POSCAR_conversions.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.4.2._POSCAR_conversions.html#2.-System.dump(‘poscar’)">2. System.dump(‘poscar’)</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.4.2._POSCAR_conversions.html#3.-atomman.load(‘poscar’)">3. atomman.load(‘poscar’)</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="1.4.3._CIF_conversions.html">1.4.3. CIF conversions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="1.4.3._CIF_conversions.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.4.3._CIF_conversions.html#2.-atomman.load(‘cif’)">2. atomman.load(‘cif’)</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="1.4.4._table_conversions.html">1.4.4. table conversions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="1.4.4._table_conversions.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.4.4._table_conversions.html#2.-System.dump(‘table’)">2. System.dump(‘table’)</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.4.4._table_conversions.html#3.-atomman.load(‘table’)">3. atomman.load(‘table’)</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="1.4.5._LAMMPS_data_file_conversions.html">1.4.5. LAMMPS data file conversions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="1.4.5._LAMMPS_data_file_conversions.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.4.5._LAMMPS_data_file_conversions.html#2.-atomman.load(‘atom_data’)">2. atomman.load(‘atom_data’)</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.4.5._LAMMPS_data_file_conversions.html#3.-System.dump(‘atom_data’)">3. System.dump(‘atom_data’)</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="1.4.6._LAMMPS_dump_file_conversions.html">1.4.6. LAMMPS dump file conversions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="1.4.6._LAMMPS_dump_file_conversions.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.4.6._LAMMPS_dump_file_conversions.html#2.-System.dump(‘atom_dump’)">2. System.dump(‘atom_dump’)</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.4.6._LAMMPS_dump_file_conversions.html#3.-atomman.load(‘atom_dump’)">3. atomman.load(‘atom_dump’)</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="1.4.7._ase_and_phonopy_conversions.html">1.4.7. ase and phonopy conversions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="1.4.7._ase_and_phonopy_conversions.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.4.7._ase_and_phonopy_conversions.html#2.-System.dump(‘ase_Atoms’)-and-System.dump(‘phonopy_Atoms’)">2. System.dump(‘ase_Atoms’) and System.dump(‘phonopy_Atoms’)</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.4.7._ase_and_phonopy_conversions.html#3.-atomman.load(‘ase_Atoms’)-and-atomman.load(‘phonopy_Atoms’)">3. atomman.load(‘ase_Atoms’) and atomman.load(‘phonopy_Atoms’)</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="1.4.8._pymatgen_conversions.html">1.4.8. pymatgen conversions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="1.4.8._pymatgen_conversions.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.4.8._pymatgen_conversions.html#2.-System.dump(‘pymatgen_Structure’)">2. System.dump(‘pymatgen_Structure’)</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.4.8._pymatgen_conversions.html#3.-atomman.load(‘pymatgen_Structure’)">3. atomman.load(‘pymatgen_Structure’)</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="1.4.9._spglib_conversions.html">1.4.9. spglib conversions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="1.4.9._spglib_conversions.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.4.9._spglib_conversions.html#2.-System.dump(‘spglib_cell’)">2. System.dump(‘spglib_cell’)</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.4.9._spglib_conversions.html#3.-atomman.load(‘spglib_cell’)">3. atomman.load(‘spglib_cell’)</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="1.4.10._prototype_loading.html">1.4.10. prototype loading</a><ul>
<li class="toctree-l2"><a class="reference internal" href="1.4.10._prototype_loading.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.4.10._prototype_loading.html#2.-atomman.load(‘prototype’)">2. atomman.load(‘prototype’)</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="1.4.11._crystal_loading.html">1.4.11. crystal loading</a><ul>
<li class="toctree-l2"><a class="reference internal" href="1.4.11._crystal_loading.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.4.11._crystal_loading.html#2.-atomman.load(‘crystal’)">2. atomman.load(‘crystal’)</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="1.4.12._DFT_reference_crystal_loading.html">1.4.12. DFT reference crystal loading</a><ul>
<li class="toctree-l2"><a class="reference internal" href="1.4.12._DFT_reference_crystal_loading.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.4.12._DFT_reference_crystal_loading.html#2.-atomman.load(‘prototype’)">2. atomman.load(‘prototype’)</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="1.5._Settings_and_databases.html">1.5. Settings and databases</a><ul>
<li class="toctree-l2"><a class="reference internal" href="1.5._Settings_and_databases.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.5._Settings_and_databases.html#2.-Settings">2. Settings</a></li>
<li class="toctree-l2"><a class="reference internal" href="1.5._Settings_and_databases.html#3.-Database-interface">3. Database interface</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="2._LAMMPS_functionality.html">2. LAMMPS functionality</a><ul>
<li class="toctree-l2"><a class="reference internal" href="2._LAMMPS_functionality.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="2._LAMMPS_functionality.html#2.-Interatomic-Potential-Control">2. Interatomic Potential Control</a></li>
<li class="toctree-l2"><a class="reference internal" href="2._LAMMPS_functionality.html#3.-Generate-initial-system">3. Generate initial system</a></li>
<li class="toctree-l2"><a class="reference internal" href="2._LAMMPS_functionality.html#4.-Converting-to/from-LAMMPS-units">4. Converting to/from LAMMPS units</a></li>
<li class="toctree-l2"><a class="reference internal" href="2._LAMMPS_functionality.html#5.-Composing-LAMMPS-Input-Scripts">5. Composing LAMMPS Input Scripts</a></li>
<li class="toctree-l2"><a class="reference internal" href="2._LAMMPS_functionality.html#6.-Run-LAMMPS">6. Run LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="2._LAMMPS_functionality.html#7.-Analyzing-Thermo-Results">7. Analyzing Thermo Results</a></li>
<li class="toctree-l2"><a class="reference internal" href="2._LAMMPS_functionality.html#8-Reading-in-dump-files">8 Reading in dump files</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="2.1._Potential_class.html">2.1. Potential class</a><ul>
<li class="toctree-l2"><a class="reference internal" href="2.1._Potential_class.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="2.1._Potential_class.html#2.-Loading-LAMMPS-Potentials">2. Loading LAMMPS Potentials</a></li>
<li class="toctree-l2"><a class="reference internal" href="2.1._Potential_class.html#3.-Potential-Classes">3. Potential Classes</a></li>
<li class="toctree-l2"><a class="reference internal" href="2.1._Potential_class.html#4.-Building-a-new-potential">4. Building a new potential</a></li>
<li class="toctree-l2"><a class="reference internal" href="2.1._Potential_class.html#5.-potential_LAMMPS-Data-Model">5. potential_LAMMPS Data Model</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="2.2._Running_LAMMPS_and_the_Log_class.html">2.2. Running LAMMPS and the Log class</a><ul>
<li class="toctree-l2"><a class="reference internal" href="2.2._Running_LAMMPS_and_the_Log_class.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="2.2._Running_LAMMPS_and_the_Log_class.html#2.-Running-LAMMPS">2. Running LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="2.2._Running_LAMMPS_and_the_Log_class.html#3.-Accessing-results-with-Log-class">3. Accessing results with Log class</a></li>
<li class="toctree-l2"><a class="reference internal" href="2.2._Running_LAMMPS_and_the_Log_class.html#4.-Restarting-and-flattening">4. Restarting and flattening</a></li>
<li class="toctree-l2"><a class="reference internal" href="2.2._Running_LAMMPS_and_the_Log_class.html#5.-Error-messages">5. Error messages</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="3._Basic_support_and_analysis_tools.html">3. Basic support and analysis tools</a><ul>
<li class="toctree-l2"><a class="reference internal" href="3._Basic_support_and_analysis_tools.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="3._Basic_support_and_analysis_tools.html#2.-Elastic-constants">2. Elastic constants</a></li>
<li class="toctree-l2"><a class="reference internal" href="3._Basic_support_and_analysis_tools.html#3.-Relative-distances-between-atoms">3. Relative distances between atoms</a></li>
<li class="toctree-l2"><a class="reference internal" href="3._Basic_support_and_analysis_tools.html#4.-Region-selectors">4. Region selectors</a></li>
<li class="toctree-l2"><a class="reference internal" href="3._Basic_support_and_analysis_tools.html#5.-Basic-tools">5. Basic tools</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="3.1._ElasticConstants_class.html">3.1. ElasticConstants class</a><ul>
<li class="toctree-l2"><a class="reference internal" href="3.1._ElasticConstants_class.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="3.1._ElasticConstants_class.html#2.-Elastic-constants-representations">2. Elastic constants representations</a></li>
<li class="toctree-l2"><a class="reference internal" href="3.1._ElasticConstants_class.html#3.-Setting-values">3. Setting values</a></li>
<li class="toctree-l2"><a class="reference internal" href="3.1._ElasticConstants_class.html#4.-ElasticConstants.tranform()">4. ElasticConstants.tranform()</a></li>
<li class="toctree-l2"><a class="reference internal" href="3.1._ElasticConstants_class.html#5.-Shear-and-bulk-modulus-estimates">5. Shear and bulk modulus estimates</a></li>
<li class="toctree-l2"><a class="reference internal" href="3.1._ElasticConstants_class.html#6.-Crystal-system-normalized-values">6. Crystal system normalized values</a></li>
<li class="toctree-l2"><a class="reference internal" href="3.1._ElasticConstants_class.html#7.-ElasticConstants.model()">7. ElasticConstants.model()</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="3.2._NeighborList_class.html">3.2. NeighborList class</a><ul>
<li class="toctree-l2"><a class="reference internal" href="3.2._NeighborList_class.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="3.2._NeighborList_class.html#2.-Identifying-neighbors">2. Identifying neighbors</a></li>
<li class="toctree-l2"><a class="reference internal" href="3.2._NeighborList_class.html#3.-build()">3. build()</a></li>
<li class="toctree-l2"><a class="reference internal" href="3.2._NeighborList_class.html#4.-dump()-and-load()">4. dump() and load()</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="3.3._Region_selectors.html">3.3. Region selectors</a><ul>
<li class="toctree-l2"><a class="reference internal" href="3.3._Region_selectors.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="3.3._Region_selectors.html#2.-Plane-slicing">2. Plane slicing</a></li>
<li class="toctree-l2"><a class="reference internal" href="3.3._Region_selectors.html#3.-Volume-selection">3. Volume selection</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="3.4._Minimum_energy_paths.html">3.4. Minimum energy paths</a><ul>
<li class="toctree-l2"><a class="reference internal" href="3.4._Minimum_energy_paths.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="3.4._Minimum_energy_paths.html#2.-Theory-and-Methodology">2. Theory and Methodology</a></li>
<li class="toctree-l2"><a class="reference internal" href="3.4._Minimum_energy_paths.html#3.-BasePath-class-and-common-setup">3. BasePath class and common setup</a></li>
<li class="toctree-l2"><a class="reference internal" href="3.4._Minimum_energy_paths.html#4.-ISMPath">4. ISMPath</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="3.5._Cluster_generators.html">3.5. Cluster generators</a><ul>
<li class="toctree-l2"><a class="reference internal" href="3.5._Cluster_generators.html#1.-BondAngleMap">1. BondAngleMap</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="4._Defect_creation_and_analysis.html">4. Defect creation and analysis</a><ul>
<li class="toctree-l2"><a class="reference internal" href="4._Defect_creation_and_analysis.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="4._Defect_creation_and_analysis.html#2.-Point-defects">2. Point defects</a></li>
<li class="toctree-l2"><a class="reference internal" href="4._Defect_creation_and_analysis.html#3.-Free-surfaces">3. Free surfaces</a></li>
<li class="toctree-l2"><a class="reference internal" href="4._Defect_creation_and_analysis.html#4.-Stacking-faults">4. Stacking faults</a></li>
<li class="toctree-l2"><a class="reference internal" href="4._Defect_creation_and_analysis.html#5.-Dislocations">5. Dislocations</a></li>
<li class="toctree-l2"><a class="reference internal" href="4._Defect_creation_and_analysis.html#6.-Strain-class">6. Strain class</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="4.1._Point_defect_generation.html">4.1. Point defect generation</a><ul>
<li class="toctree-l2"><a class="reference internal" href="4.1._Point_defect_generation.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.1._Point_defect_generation.html#2.-atomman.defect.vacancy()">2. atomman.defect.vacancy()</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.1._Point_defect_generation.html#3.-atomman.defect.interstitial()">3. atomman.defect.interstitial()</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.1._Point_defect_generation.html#4.-atomman.defect.substitutional()">4. atomman.defect.substitutional()</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.1._Point_defect_generation.html#5.-atomman.defect.dumbbell()">5. atomman.defect.dumbbell()</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.1._Point_defect_generation.html#6.-atomman.defect.point()">6. atomman.defect.point()</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="4.2._Free_surface_generator.html">4.2. Free surface generator</a><ul>
<li class="toctree-l2"><a class="reference internal" href="4.2._Free_surface_generator.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.2._Free_surface_generator.html#2.-Theory">2. Theory</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.2._Free_surface_generator.html#3.-Class-basics">3. Class basics</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.2._Free_surface_generator.html#4.-Examples">4. Examples</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="4.3._Stacking_fault_generator.html">4.3. Stacking fault generator</a><ul>
<li class="toctree-l2"><a class="reference internal" href="4.3._Stacking_fault_generator.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.3._Stacking_fault_generator.html#2.-Theory">2. Theory</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.3._Stacking_fault_generator.html#3.-Class-basics">3. Class basics</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.3._Stacking_fault_generator.html#4.-Examples">4. Examples</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="4.4._Dislocation_solution_and_generator.html">4.4. Dislocation solution and generator</a><ul>
<li class="toctree-l2"><a class="reference internal" href="4.4._Dislocation_solution_and_generator.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.4._Dislocation_solution_and_generator.html#2.-Theory">2. Theory</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.4._Dislocation_solution_and_generator.html#3.-Volterra-solutions">3. Volterra solutions</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.4._Dislocation_solution_and_generator.html#4.-Dislocation-initialization">4. Dislocation initialization</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.4._Dislocation_solution_and_generator.html#5.-Dislocation-Monopole-Configuration">5. Dislocation Monopole Configuration</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.4._Dislocation_solution_and_generator.html#6.-Periodic-Array-of-Dislocations-Configuration">6. Periodic Array of Dislocations Configuration</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="4.5._Gamma_surface_plotting.html">4.5. Gamma surface plotting</a><ul>
<li class="toctree-l2"><a class="reference internal" href="4.5._Gamma_surface_plotting.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.5._Gamma_surface_plotting.html#2.-Underlying-theory">2. Underlying theory</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.5._Gamma_surface_plotting.html#3.-Defining-gamma-surface-data">3. Defining gamma surface data</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.5._Gamma_surface_plotting.html#4.-Plotting-methods">4. Plotting methods</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.5._Gamma_surface_plotting.html#5.-Minimum-energy-slip-path">5. Minimum energy slip path</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.5._Gamma_surface_plotting.html#6.-Utility-methods">6. Utility methods</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="4.6._Dislocation_analysis_tools.html">4.6. Dislocation analysis tools</a><ul>
<li class="toctree-l2"><a class="reference internal" href="4.6._Dislocation_analysis_tools.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.6._Dislocation_analysis_tools.html#1.1.-Load-atomic-systems">1.1. Load atomic systems</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.6._Dislocation_analysis_tools.html#2.-Slip-vector">2. Slip vector</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.6._Dislocation_analysis_tools.html#3.-Disregistry">3. Disregistry</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.6._Dislocation_analysis_tools.html#4.-Nye-tensor">4. Nye tensor</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.6._Dislocation_analysis_tools.html#5.-Differential-displacement-maps">5. Differential displacement maps</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="4.7._Semidiscrete_variational_Peierls-Nabarro_model.html">4.7. Semidiscrete variational Peierls-Nabarro model</a><ul>
<li class="toctree-l2"><a class="reference internal" href="4.7._Semidiscrete_variational_Peierls-Nabarro_model.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.7._Semidiscrete_variational_Peierls-Nabarro_model.html#2.-Theory">2. Theory</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.7._Semidiscrete_variational_Peierls-Nabarro_model.html#3.-Methodology-overview">3. Methodology overview</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.7._Semidiscrete_variational_Peierls-Nabarro_model.html#4.-Initialize-SDVPN-using-GammaSurface-and-VolterraDislocation">4. Initialize SDVPN using GammaSurface and VolterraDislocation</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.7._Semidiscrete_variational_Peierls-Nabarro_model.html#5.-Generate-initial-disregistry">5. Generate initial disregistry</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.7._Semidiscrete_variational_Peierls-Nabarro_model.html#6.-Solve-SDVPN-model">6. Solve SDVPN model</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.7._Semidiscrete_variational_Peierls-Nabarro_model.html#7.-Save-and-load-results">7. Save and load results</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.7._Semidiscrete_variational_Peierls-Nabarro_model.html#8.-Peierls-stress-estimates">8. Peierls stress estimates</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="4.8._Strain_class.html">4.8. Strain class</a><ul>
<li class="toctree-l2"><a class="reference internal" href="4.8._Strain_class.html#1.-Introduction">1. Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.8._Strain_class.html#2.-Theory">2. Theory</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.8._Strain_class.html#3.-Calculation-parameter-options">3. Calculation parameter options</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.8._Strain_class.html#4.-Strain-class">4. Strain class</a></li>
<li class="toctree-l2"><a class="reference internal" href="4.8._Strain_class.html#5.-Plotting">5. Plotting</a></li>
</ul>
</li>
</ul>
</div>
</div>


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